INSTALLATION
Multiple packages are either required or suggested for HitWalker to be installed and the main ones can be retrieved from the following two sources:
From inside R use the following commands:
The Comprehensive R Archive Network using:
install.packages(c("igraph", "RSQLite", "cgdsr", "reshape2"))
Bioconductor using:
source("http://bioconductor.org/biocLite.R")
biocLite(c("graph", "Rgraphviz", "Streamer", "biomaRt"))
Note that of these packages Rgraphviz is the most difficult to install due to its dependence on the graphviz external library. Please see the documentation at: http://www.bioconductor.org/packages/2.10/bioc/readmes/Rgraphviz/README for installation instructions for your platform.
When these dependencies are met, HitWalker can be installed from within R using the following commands:
Linux, Mac OSX or Windows (assuming you are in the appropriate directory):
install.packages("HitWalker_0.99.0.tar.gz", repos=NULL, type="source")
Also, the accompanying HitWalkerData package should be installed as well.
install.packages("HitWalkerData_0.99.0.tar.gz", repos=NULL, type="source")
Note that HitWalker has currently only been tested thoroughly on R version R-2.15.1 using a 64-bit Ubuntu Linux machine.
Once installed, the package can be loaded and the user can familiarize themselves with its use by reading any of the four supplied vignettes. The vignettes build on
each other and so the suggested reading order is:
Hitwalker_Create_DB
Hitwalker_Add_metadata
Hitwalker_glio
HitWalker
First load the package:
library(HitWalker)
library(HitWalkerData)
Vignettes can be examined through a command similar to:
vignette("Hitwalker_Create_DB")
Similarly, all the vignettes can be listed by typing:
vignette(package="HitWalker")
To generate an executable file called 'HitWalker.R' containing all the code in the vignette carry out a command similar to:
Stangle(system.file("doc/HitWalker.Rnw", package="HitWalker"))
Where 'HitWalker.Rnw' can be any of the supplied vignettes.
From the Stangle command a file called 'HitWalker.R' will be produced and can be executed section by section or all at once by:
source("HitWalker.R")
See the R documentation at http://cran.r-project.org/ for general use of the R programming language.